Samtools implements various utilities for post-processing alignments in the
SAM, BAM, and CRAM formats, including indexing, variant calling (in conjunction
with bcftools), and a simple alignment viewer.

Log message:
samtools: updated to 1.9
Release 1.9:
* Samtools mpileup VCF and BCF output is now deprecated. It is still
functional, but will warn. Please use bcftools mpileup instead.
* Samtools mpileup now handles the '-d' max_depth option differently. There
is no longer an enforced minimum, and '-d 0' is interpreted as limitless
(no maximum - warning this may be slow). The default per-file depth is
now 8000, which matches the value mpileup used to use when processing
a single sample. To get the previous default behaviour use the higher
of 8000 divided by the number of samples across all input files, or 250.
* Samtools stats new features:
- The '--remove-overlaps' option discounts overlapping portions of
templates when computing coverage and mapped base counting.
- When a target file is in use, the number of bases inside the
target is printed and the percentage of target bases with coverage
above a given threshold specified by the '--cov-threshold' option.
- Split base composition and length statistics by first and last reads.
* Samtools faidx new features:
- Now takes long options.
- Now warns about zero-length and truncated sequences due to the
requested range being beyond the end of the sequence.
- Gets a new option (--continue) that allows it to carry on
when a requested sequence was not in the index.
- It is now possible to supply the list of regions to output in a text
file using the new '--region-file' option.
- New '-i' option to make faidx return the reverse complement of
the regions requested.
- faidx now works on FASTQ (returning FASTA) and added a new
fqidx command to index and return FASTQ.
* Samtools collate now has a fast option '-f' that only operates on
primary pairs, dropping secondary and supplementary. It tries to write
pairs to the final output file as soon as both reads have been found.
* Samtools bedcov gets a new '-j' option to make it ignore deletions (D) and
reference skips (N) when computing coverage.
* Small speed up to samtools coordinate sort, by converting it to use
radix sort.
* Samtools idxstats now works on SAM and CRAM files, however this
isn't fast due to some information lacking from indices.
* Compression levels may now be specified with the level=N
output-fmt-option. E.g. with -O bam,level=3.
* Various documentation improvements.
* Bug-fixes:
- Improved error reporting in several places.
- Various test improvements.
- Fixed failures in the multi-region iterator (view -M) when regions
provided via BED files include overlaps
- Samtools stats now counts '=' and 'X' CIGAR operators when
counting mapped bases.
- Samtools stats has fixes for insert size filtering (-m, -i).
- Samtools stats -F now longer negates an earlier -d option.
- Fix samtools stats crash when using a target region.
- Samtools sort now keeps to a single thread when the -@ option is absent.
Previously it would spawn a writer thread, which could cause the CPU
usage to go slightly over 100%.
- Fixed samtools phase '-A' option which was incorrectly defined to take
a parameter.
- Fixed compilation problems when using C_INCLUDE_PATH.
- Fixed --version when built from a Git repository.
- Use noenhanced mode for title in plot-bamstats. Prevents unwanted
interpretation of characters like underscore in gnuplot version 5.
- blast2sam.pl now reports perfect match hits (no indels or mismatches).
- Fixed bug in fasta and fastq subcommands where stdout would not be flushed
correctly if the -0 option was used.
- Fixed invalid memory access in mpileup and depth on alignment records
where the sequence is absent.